GemCell:
A Generic Platform for Modeling
Multi-Cellular Biological Systems
Hila Amir-Kroll, Avital Sadot, Irun R. Cohen and David Harel
The mass and complexity of biological information requires
computer-aided
simulation and analysis to help scientists
achieve understanding and guide
experimentation. Although living organisms are composed of cells, actual genomic
and proteomic data has not yet led to a satisfactory model of working cell in-silico.
We have set out to devise a
user-friendly generic platform, GemCell, for Generic
Executable Modeling of Cells, based on whole, functioning cells.
Starting with
the
cell simplifies life, because all cells expresses essentially five generic types
of
behavior: replication,
death, movement (including change of shape and
adherence),
export (secretion, signaling, etc.) and import (receiving
signals, metabolites, phagocytosis, etc.). The details of these behaviors are specified in GemCell for
particular kinds
of cells as part of a database of biological specifics (the
DBS), which
specifies the cell properties and functions that
depend on the cell’s history,
state,
environment, etc. The DBS is designed in an intuitive fashion, so users are able
to
easily insert their data of interest. The generic part of GemCell, built using
Statecharts, is a fully dynamic model of a
cell, its interactions with the
environment
and its resulting behavior, individually and collectively. Model specificity
emerges
from the DBS, so that model execution is carried out by the statecharts
executing with
the aid of specific
data extracted from the DBS dynamically. Our long term goal
is
for GemCell to serve as a broadly applicable
platform for biological modeling
and
analysis, supporting user-friendly in-silico experimentation, animation,
discovery of
emergent properties, and hypothesis testing, for a wide variety of biological
systems.
Structure of GemCell: The GemCell model is a
combination of
generic biology, formed by five generic laws of inter-cellular behavior,
and specific biology, built from the data of actual cellular systems.
GemCell consists of three components: the generic state-based model,
which models the generic biology; the DBS, which holds the information
about the specific cellular system that the user wishes to model;
and the output of the system’s dynamics that emerges from the execution
of the generic model combined with the DBS. These three components
are integrated and operate together continuously during model execution.
* See full paper in :
H. Amir-Kroll, A. Sadot, I.R. Cohen and D. Harel,
"GemCell: A Generic Platform for Modeling Multi-Cellular
Biological Systems", Electronic Notes in Theoret. Comput. Sci.,
in press.